IGV_get_bam/workflow.wdl

import "./tasks/getBam.wdl" as getBam


workflow {{ project_name }} {
	File inputRegionsFile
	Array[Array[File]] inputRegions = read_tsv(inputRegionsFile)
	File bam
	File bam_idx
	String sample
	String docker
	String cluster_config
	String disk_size

	scatter (Region in inputRegions) {
		call getBam.getBam as getBam {
			input:	
			bam=bam,
			bam_idx=bam_idx,
			sample=sample,
			region=Region[0],
			docker=docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}
}